Seasonal and spatial phytoplankton distribution in relation to environmental factors was investigated in New Mangalore Port, a major port along the west coast of India. A well-mixed water column characterized the non-monsoon seasons, whereas it was weakly stratified during monsoon. Water quality index (TRIX) scores indicated good water quality except during pre-monsoon (inner zone surface) and monsoon (near bottom waters). Surface abundance of tychopelagic diatoms ( Paralia sulcata , Melosira nummuloides , Cylindrotheca closterium , and Nitzschia sigma ) was higher during non-monsoon seasons. Certain centric diatoms, e.g., Leptocylindrus danicus , P. sulcata , and Rhizosolenia imbricata , dominated during pre-monsoon (inner zone) and positively correlated with TRIX. High Skeletonema costatum and dinoflagellate abundance during the monsoon season coincided with high nutrient concentrations. Five potential toxic and fourteen harmful/bloom forming algal species were encountered at abundances below the level that can be considered as harmful to the ecosystem. In addition to a baseline database, this study highlights the potential use of certain diatom species as indicators of hydrography and water quality for monitoring dynamic coastal marine ecosystems.